+Open data
-Basic information
Entry | Database: PDB / ID: 2e3w | ||||||
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Title | X-ray structure of native RNase A | ||||||
Components | Ribonuclease pancreaticPancreatic ribonuclease family | ||||||
Keywords | HYDROLASE / alpha-helix / beta-sheet | ||||||
Function / homology | Function and homology information pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å | ||||||
Authors | Boerema, D.J. / Tereshko, V.A. / Kent, S.B.H. | ||||||
Citation | Journal: Biopolymers / Year: 2008 Title: Total synthesis by modern chemical ligation methods and high resolution (1.1 A) X-ray structure of ribonuclease A Authors: Boerema, D.J. / Tereshko, V.A. / Kent, S.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e3w.cif.gz | 58.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e3w.ent.gz | 42.7 KB | Display | PDB format |
PDBx/mmJSON format | 2e3w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/2e3w ftp://data.pdbj.org/pub/pdb/validation_reports/e3/2e3w | HTTPS FTP |
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-Related structure data
Related structure data | 2nuiC 1izpS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.4 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.89 Details: Well solution: Combination of Hampton Index Reagents 3 and 9, Final solution: 0.1 M Bis-tris, 1.0 M ammonium sulfate, 1.5 M NaCl, pH 5.89, Drop: 2 microliter well solution + 2 microliter 10 ...Details: Well solution: Combination of Hampton Index Reagents 3 and 9, Final solution: 0.1 M Bis-tris, 1.0 M ammonium sulfate, 1.5 M NaCl, pH 5.89, Drop: 2 microliter well solution + 2 microliter 10 mg/ml protein solution in water, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9002 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 15, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9002 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→50 Å / Num. obs: 69871 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1IZP Resolution: 1.05→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.656 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.424 Å2
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Refinement step | Cycle: LAST / Resolution: 1.05→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.05→1.077 Å / Total num. of bins used: 20
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